tlo.methods.hiv module ====================== .. automodule:: tlo.methods.hiv .. autoclass:: Hiv Bases: :class:`tlo.core.Module` **PARAMETERS:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - time_inf - DATA_FRAME - prob of time since infection for baseline adult pop * - art_coverage - DATA_FRAME - coverage of ART at baseline * - treatment_cascade - DATA_FRAME - spectrum estimates of treatment cascade * - beta - REAL - Transmission rate * - unaids_prevalence_adjustment_factor - REAL - adjustment for baseline age-specific prevalence values to give correct population prevalence * - prob_mtct_untreated - REAL - Probability of mother to child transmission * - prob_mtct_treated - REAL - Probability of mother to child transmission, mother on ART * - prob_mtct_incident_preg - REAL - Probability of mother to child transmission, mother infected during pregnancy * - monthly_prob_mtct_bf_untreated - REAL - Probability of mother to child transmission during breastfeeding * - monthly_prob_mtct_bf_treated - REAL - Probability of mother to child transmission, mother infected during breastfeeding * - rr_fsw - REAL - Relative risk of HIV with female sex work * - rr_circumcision - REAL - Relative risk of HIV with circumcision * - rr_rural - REAL - Relative risk of HIV in rural location * - rr_windex_poorer - REAL - Relative risk of HIV with wealth level poorer * - rr_windex_middle - REAL - Relative risk of HIV with wealth level middle * - rr_windex_richer - REAL - Relative risk of HIV with wealth level richer * - rr_windex_richest - REAL - Relative risk of HIV with wealth level richest * - rr_sex_f - REAL - Relative risk of HIV if female * - rr_edlevel_primary - REAL - Relative risk of HIV with primary education * - rr_edlevel_secondary - REAL - Relative risk of HIV with secondary education * - rr_edlevel_higher - REAL - Relative risk of HIV with higher education * - rr_behaviour_change - REAL - Relative risk of HIV with behaviour modification * - proportion_reduction_in_risk_of_hiv_aq_if_on_prep - REAL - Proportion reduction in risk of HIV acquisition if on PrEP. 0 for no efficacy; 1.0 for perfect efficacy. * - mean_months_between_aids_and_death - REAL - Mean number of months (distributed exponentially) for the time between AIDS and AIDS Death * - mean_months_between_aids_and_death_infant - REAL - Mean number of months for the time between AIDS and AIDS Death for infants * - infection_to_death_weibull_shape_1519 - REAL - Shape parameter for Weibull describing time between infection and death for 15-19 yo (units: years) * - infection_to_death_weibull_shape_2024 - REAL - Shape parameter for Weibull describing time between infection and death for 20-24 yo (units: years) * - infection_to_death_weibull_shape_2529 - REAL - Shape parameter for Weibull describing time between infection and death for 25-29 yo (units: years) * - infection_to_death_weibull_shape_3034 - REAL - Shape parameter for Weibull describing time between infection and death for 30-34 yo (units: years) * - infection_to_death_weibull_shape_3539 - REAL - Shape parameter for Weibull describing time between infection and death for 35-39 yo (units: years) * - infection_to_death_weibull_shape_4044 - REAL - Shape parameter for Weibull describing time between infection and death for 40-44 yo (units: years) * - infection_to_death_weibull_shape_4549 - REAL - Shape parameter for Weibull describing time between infection and death for 45-49 yo (units: years) * - infection_to_death_weibull_scale_1519 - REAL - Scale parameter for Weibull describing time between infection and death for 15-19 yo (units: years) * - infection_to_death_weibull_scale_2024 - REAL - Scale parameter for Weibull describing time between infection and death for 20-24 yo (units: years) * - infection_to_death_weibull_scale_2529 - REAL - Scale parameter for Weibull describing time between infection and death for 25-29 yo (units: years) * - infection_to_death_weibull_scale_3034 - REAL - Scale parameter for Weibull describing time between infection and death for 30-34 yo (units: years) * - infection_to_death_weibull_scale_3539 - REAL - Scale parameter for Weibull describing time between infection and death for 35-39 yo (units: years) * - infection_to_death_weibull_scale_4044 - REAL - Scale parameter for Weibull describing time between infection and death for 40-44 yo (units: years) * - infection_to_death_weibull_scale_4549 - REAL - Scale parameter for Weibull describing time between infection and death for 45-49 yo (units: years) * - art_default_to_aids_mean_years - REAL - Mean years between when a person (any change) stops being on treatment to when AIDS is onset (if the absence of resuming treatment). * - prop_delayed_aids_onset - REAL - Proportion of PLHIV that will have delayed AIDS onset to compensate for AIDS-TB * - mean_survival_for_infants_infected_prior_to_birth - REAL - Exponential rate parameter for mortality in infants who are infected before birth * - infection_to_death_infant_infection_after_birth_weibull_scale - REAL - Weibull scale parameter for mortality in infants who are infected after birth * - infection_to_death_infant_infection_after_birth_weibull_shape - REAL - Weibull shape parameter for mortality in infants who are infected after birth * - hiv_testing_rates - DATA_FRAME - annual rates of testing for children and adults * - rr_test_hiv_positive - REAL - relative likelihood of having HIV test for people with HIV * - hiv_testing_rate_adjustment - REAL - adjustment to current testing rates to account for multiple routes into HIV testing * - treatment_initiation_adjustment - REAL - adjustment to current ART coverage levels to account for defaulters * - vs_adjustment - REAL - adjustment to current viral suppression levels to account for defaulters * - prob_hiv_test_at_anc_or_delivery - REAL - probability of a women having hiv test at anc or following delivery * - prob_hiv_test_for_newborn_infant - REAL - probability of a newborn infant having HIV test pre-discharge * - prob_start_art_or_vs - REAL - Probability that a person will start treatment and be virally suppressed following testing * - prob_behav_chg_after_hiv_test - REAL - Probability that a person will change risk behaviours, if HIV-negative, following testing * - prob_prep_for_fsw_after_hiv_test - REAL - Probability that a FSW will start PrEP, if HIV-negative, following testing * - prob_prep_for_agyw - REAL - Probability that adolescent girls / young women will start PrEP * - prob_circ_after_hiv_test - REAL - Probability that a male will be circumcised, if HIV-negative, following testing * - prob_circ_for_child_before_2020 - REAL - Probability that a male aging <15 yrs will be circumcised before year 2020 * - prob_circ_for_child_from_2020 - REAL - Probability that a male aging <15 yrs will be circumcised from year 2020, which is different from before 2020 as children vmmc policy/fund/cases has changed, according to PEPFAR 2020 Country Operational Plan and DHIS2 data * - probability_of_being_retained_on_prep_every_3_months - REAL - Probability that someone who has initiated on prep will attend an appointment and be on prep for the next 3 months, until the next appointment. * - probability_of_being_retained_on_art_every_3_months - REAL - Probability that someone who has initiated on treatment will attend an appointment and be on treatment for next 3 months, until the next appointment. * - probability_of_seeking_further_art_appointment_if_drug_not_available - REAL - Probability that a person who 'should' be on art will seek another appointment (the following day and try for each of the next 7 days) if drugs were not available. * - probability_of_seeking_further_art_appointment_if_appointment_not_available - REAL - Probability that a person who 'should' be on art will seek another appointment if the health-system has not been able to provide them with an appointment * - prep_start_year - REAL - Year from which PrEP is available * - ART_age_cutoff_young_child - INT - Age cutoff for ART regimen for young children * - ART_age_cutoff_older_child - INT - Age cutoff for ART regimen for older children * - rel_probability_art_baseline_aids - REAL - relative probability of person with HIV infection over 10 years being on ART at baseline * - aids_tb_treatment_adjustment - REAL - probability of death if aids and tb, person on treatment for tb * - dispensation_period_months - REAL - length of prescription for ARVs in months, same for all PLHIV **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - hv_inf - BOOL - Is person currently infected with HIV (NB. AIDS status is determined by prescence of the AIDS Symptom. * - hv_art - CATEGORICAL - ART status of person, whether on ART or not; and whether viral load is suppressed or not if on ART.. Possible values are: [not, on_VL_suppressed, on_not_VL_suppressed, ] * - hv_on_cotrimoxazole - BOOL - Whether the person is currently taking and receiving a malaria-protective effect from cotrimoxazole * - hv_is_on_prep - BOOL - Whether the person is currently taking and receiving a protective effect from Pre-Exposure Prophylaxis * - hv_behaviour_change - BOOL - Has this person been exposed to HIV prevention counselling following a negative HIV test result * - hv_diagnosed - BOOL - Knows that they are HIV+: i.e. is HIV+ and tested as HIV+ * - hv_number_tests - INT - Number of HIV tests ever taken * - hv_last_test_date - DATE - Date of last HIV test * - hv_date_inf - DATE - Date infected with HIV * - hv_date_treated - DATE - date hiv treatment started * - hv_date_last_ART - DATE - date of last ART dispensation **Class attributes:** ADDITIONAL_DEPENDENCIES : {'Tb', 'NewbornOutcomes'} CAUSES_OF_DEATH : {'AIDS_non_TB': , 'AIDS_TB': } CAUSES_OF_DISABILITY : {'HIV': } INIT_DEPENDENCIES : {'SymptomManager', 'HealthSystem', 'Demography', 'Lifestyle'} METADATA : {, , , } OPTIONAL_INIT_DEPENDENCIES : {'HealthBurden'} **Functions (defined or overridden in class Hiv):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: pre_initialise_population .. automethod:: initialise_population .. automethod:: initialise_baseline_prevalence .. automethod:: initialise_baseline_art .. automethod:: initialise_baseline_tested .. automethod:: initialise_simulation .. automethod:: on_birth .. automethod:: report_daly_values .. automethod:: mtct_during_breastfeeding .. automethod:: do_new_infection .. automethod:: sample_time_from_infection_to_aids_given_parameters .. automethod:: get_time_from_infection_to_aids_distribution_parameters .. automethod:: get_time_from_aids_to_death .. automethod:: do_when_hiv_diagnosed .. automethod:: prob_art_start_after_test .. automethod:: prob_viral_suppression .. automethod:: stops_treatment .. automethod:: per_capita_testing_rate .. automethod:: decide_whether_hiv_test_for_mother .. automethod:: decide_whether_hiv_test_for_infant .. automethod:: check_config_of_properties .. autoclass:: HivRegularPollingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HivRegularPollingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HivInfectionEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HivInfectionEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HivInfectionDuringBreastFeedingEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HivInfectionDuringBreastFeedingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HivAidsOnsetEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HivAidsOnsetEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HivAidsDeathEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HivAidsDeathEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HivAidsTbDeathEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HivAidsTbDeathEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: Hiv_DecisionToContinueOnPrEP Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class Hiv_DecisionToContinueOnPrEP):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: Hiv_DecisionToContinueTreatment Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class Hiv_DecisionToContinueTreatment):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Hiv_TestAndRefer Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Hiv_TestAndRefer):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Hiv_Circ Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Hiv_Circ):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Hiv_StartInfantProphylaxis Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Hiv_StartInfantProphylaxis):** .. automethod:: __init__ .. automethod:: apply .. automethod:: never_ran .. autoclass:: HSI_Hiv_StartOrContinueOnPrep Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Hiv_StartOrContinueOnPrep):** .. automethod:: __init__ .. automethod:: apply .. automethod:: never_ran .. autoclass:: HSI_Hiv_StartOrContinueTreatment Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** EXPECTED_APPT_FOOTPRINT : **Functions (defined or overridden in class HSI_Hiv_StartOrContinueTreatment):** .. automethod:: __init__ .. automethod:: apply .. automethod:: do_at_initiation .. automethod:: do_at_continuation .. automethod:: determine_vl_status .. automethod:: get_drugs .. automethod:: consider_tb .. automethod:: never_ran .. autoclass:: HivLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HivLoggingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HivCheckPropertiesEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HivCheckPropertiesEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: DummyHivModule Bases: :class:`tlo.core.Module` **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - hv_inf - BOOL - DUMMY version of the property for hv_inf * - hv_art - CATEGORICAL - DUMMY version of the property for hv_art.. Possible values are: [not, on_VL_suppressed, on_not_VL_suppressed, ] **Class attributes:** ALTERNATIVE_TO : {'Hiv'} INIT_DEPENDENCIES : {'Demography'} **Functions (defined or overridden in class DummyHivModule):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: on_birth